Shin Megami Tensei: Persona 3 Portable is an enhanced remake of Persona 3 and gives the player the option to play as a female character. This selection alters some aspects of the story: the first Persona gained by the Protagonist, Orpheus will have a different appearance. Igor's assistant in the Velvet Room, Elizabeth can be replaced with a male equivalent named Theodore. The gender choice also alters some aspects of the Social Link stories. In addition to the new playable character there are two new difficulty levels to select from alongside the original game's three. Persona 3 Portable only includes the story of the original Persona 3 although general changes have been made to the plot regardless of character choice.

The game's revised battle system draws on elements added in Persona 3's successor Persona 4. In combat, the player is able to directly control every character as an alternative to utilizing the game's artificial intelligence. The ability to guard has been added and allies will take fatal attacks for the Protagonist preventing his or her death. Outside of Tartarus, instead of navigating the game world by directly controlling the Protagonist the player guides an on-screen cursor around an area allowing interaction with characters and objects. The game includes the voice acting of the original game although characters are not shown in the world instead being represented by on-screen portraits. In addition, the anime cutscenes seen in the original Persona 3 have been replaced to feature in-game graphics. Shōji Meguro composed new music for Persona 3 Portable, some of the game's music is different if the female protagonist is selected.